mdtbx

Toolbox for MD simulation

• Build system quickly
• Run conventional/enhanced MD simulation
• Analyze trajectory
• Calculate Free energy

Supported Features

• Sampling

  • cMD
  • Brownian Dynamics
  • Langevin Dynamics
  • Simulated Tempering
  • Simulated Annealing
  • T-REMD
  • 2D-REMD
  • REST
  • REUS
  • US
  • FEP
  • FEP/REST
  • AWH
  • WT-Metadynamics
  • OPES
  • GaMD
  • PaCS-MD
  • SMD
  • String method
  • Weighted Ensemble

• Free energy calculation

  • MMPBSA
  • MBAR
  • WHAM
  • BAR
  • Zwanzig(FEP)
  • TI
  • Jarzynski Equality
  • ERmod

• Analysis

  • trjconv/trjcat
  • fit
  • comdist
  • comvec
  • mindist
  • rmsd
  • rmsf
  • xyz
  • PCA
  • densmap
  • tICA
  • RISM/3D-RISM
  • Elastic Network Model
  • Normal Mode analysis
  • Relaxation Mode analysis
  • Go model
  • PCA Vector visualization

• Kinetic analysis

  • MSM
  • TRAM

• Build system

  • Vacuum
  • Solution
  • Membrane
  • Protein Modeling
  • Modified Residue
  • Make index group
  • Partial Chage
  • Martini
  • QM/MM

Assumptions

• System build Tools: AMBER, PyMOL, OpenBabel
• Simulation Tools: Gromacs, AMBER, Gaussian16
• ForceField: ff14SB, TIP3P, GAFF2, Lipid21, GLYCAM06-j

Install

# for pixi users
export PIXI_FROZEN=false
pixi install
pixi run pymolrc
ln -s $PWD/.pixi/envs/default/bin/mdtbx $BIN
ln -s $PWD/.pixi/envs/default/bin/pymol $BIN

# for docker users
docker build -t mdtbx .

Update

pixi run update

Usage

# for pixi users
pixi run mdtbx ...
pixi run gmx ... # equal to pixi run mdtbx cmd gmx ...

# for docker users
docker run -it --rm mdtbx mdtbx ...
docker run -it --rm mdtbx gmx ... # equal to docker run -it --rm mdtbx mdtbx cmd gmx ...